Merge master into staging

pkgs/development/python-modules/behave/default.nix

@@ -1,23 +1,22 @@
 { stdenv, fetchPypi
-, buildPythonApplication, python, pythonAtLeast
-, mock, nose, pyhamcrest
+, buildPythonApplication, isPy27, python, pythonOlder
+, mock, nose, pathpy, pyhamcrest, pytest
 , glibcLocales, parse, parse-type, six
+, traceback2
 }:
 buildPythonApplication rec {
   pname = "behave";
   version = "1.2.6";
   name = "${pname}-${version}";
 
-  disabled = pythonAtLeast "3.6";
-
   src = fetchPypi {
     inherit pname version;
-    sha256 = "b9662327aa53294c1351b0a9c369093ccec1d21026f050c3bd9b3e5cccf81a86";
+    sha256 = "11hsz365qglvpp1m1w16239c3kiw15lw7adha49lqaakm8kj6rmr";
   };
 
-  checkInputs = [ mock nose pyhamcrest ];
+  checkInputs = [ mock nose pathpy pyhamcrest pytest ];
   buildInputs = [ glibcLocales ];
-  propagatedBuildInputs = [ parse parse-type six ];
+  propagatedBuildInputs = [ parse parse-type six ] ++ stdenv.lib.optional (pythonOlder "3.0") traceback2;
 
   postPatch = ''
     patchShebangs bin
@@ -29,7 +28,7 @@ buildPythonApplication rec {
     export LANG="en_US.UTF-8"
     export LC_ALL="en_US.UTF-8"
 
-    nosetests -x
+    pytest test tests
 
     ${python.interpreter} bin/behave -f progress3 --stop --tags='~@xfail' features/
     ${python.interpreter} bin/behave -f progress3 --stop --tags='~@xfail' tools/test-features/

pkgs/development/python-modules/bibtexparser/default.nix

@@ -1,10 +1,7 @@
 { lib
-, buildPythonPackage
-, fetchFromGitHub
-, pyparsing
-, future
-, nose
-, glibcLocales
+, buildPythonPackage, fetchFromGitHub
+, future, pyparsing
+, glibcLocales, nose
 }:
 
 buildPythonPackage rec {
@@ -19,7 +16,7 @@ buildPythonPackage rec {
     sha256 = "0lmlarkfbq2hp1wa04a62245jr2mqizqsdlgilj5aq6vy92gr6ai";
   };
 
-  propagatedBuildInputs = [ pyparsing future ];
+  propagatedBuildInputs = [ future pyparsing ];
 
   checkInputs = [ nose glibcLocales ];
 

pkgs/development/python-modules/black/default.nix

@@ -0,0 +1,23 @@
+{ stdenv, buildPythonPackage, fetchPypi, pythonOlder, attrs, click }:
+
+buildPythonPackage rec {
+  pname = "black";
+  version = "18.4a0";
+
+  disabled = pythonOlder "3.6";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "04dffr4wmzs4vf2xj0cxp03hv04x0kk06qyzx6jjrp1mq0z3n2rr";
+  };
+
+  propagatedBuildInputs = [ attrs click ];
+
+  meta = with stdenv.lib; {
+    description = "The uncompromising Python code formatter";
+    homepage    = https://github.com/ambv/black;
+    license     = licenses.mit;
+    maintainers = with maintainers; [ sveitser ];
+  };
+
+}

pkgs/development/python-modules/jieba/default.nix

@@ -0,0 +1,33 @@
+{ lib, buildPythonPackage, fetchFromGitHub, glibcLocales, python, isPy3k }:
+
+buildPythonPackage rec {
+  pname = "jieba";
+  version = "0.39";
+
+  # no tests in PyPI tarball
+  src = fetchFromGitHub {
+    owner = "fxsjy";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "0hbq0l1jbgcvm58qg4p37im4jl5a9igvq3wlhlk22pmbkbvqqgzs";
+  };
+
+  checkInputs = [ glibcLocales ];
+
+  # UnicodeEncodeError
+  doCheck = isPy3k;
+
+  # Citing https://github.com/fxsjy/jieba/issues/384: "testcases is in a mess"
+  # So just picking random ones that currently work
+  checkPhase = ''
+    export LC_ALL=en_US.UTF-8
+    ${python.interpreter} test/test.py
+    ${python.interpreter} test/test_tokenize.py
+  '';
+
+  meta = with lib; {
+    description = "Chinese Words Segementation Utilities";
+    homepage = https://github.com/fxsjy/jieba;
+    license = licenses.mit;
+  };
+}

pkgs/development/python-modules/langcodes/default.nix

@@ -0,0 +1,34 @@
+{ lib
+, buildPythonPackage
+, marisa-trie
+, pythonOlder
+, fetchPypi
+, nose
+}:
+
+buildPythonPackage rec {
+  pname = "langcodes";
+  version = "1.4.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1axdiva2qglsjmnx2ak7i6hm0yhp6kbc4lcsgn8ckwy0nq1z3kr2";
+  };
+
+  propagatedBuildInputs = [ marisa-trie ];
+
+  disabled = pythonOlder "3.3";
+
+  checkInputs = [ nose ];
+
+  checkPhase = ''
+    nosetests
+  '';
+
+  meta = with lib; {
+    description = "A toolkit for working with and comparing the standardized codes for languages, such as ‘en’ for English or ‘es’ for Spanish";
+    homepage =  http://github.com/LuminosoInsight/langcodes;
+    license = licenses.mit;
+    maintainers = with maintainers; [ ixxie ];
+  };
+}

pkgs/development/python-modules/marisa-trie/default.nix

@@ -0,0 +1,34 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, pytestrunner
+, pytest
+, hypothesis
+}:
+
+buildPythonPackage rec {
+  pname = "marisa-trie";
+  version = "0.7.4";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1n4pxnaranbh3x2fcqxwh8j1z2918vy7i4q1z4jn75m9rkm5h8ia";
+  };
+
+  postPatch = ''
+    substituteInPlace setup.py \
+      --replace "hypothesis==" "hypothesis>="
+  '';
+
+  nativeBuildInputs = [ pytestrunner ];
+
+  checkInputs = [ pytest hypothesis ];
+
+  meta = with lib; {
+    description = "Static memory-efficient Trie-like structures for Python (2.x and 3.x) based on marisa-trie C++ library";
+    longDescription = "There are official SWIG-based Python bindings included in C++ library distribution; this package provides alternative Cython-based pip-installable Python bindings.";
+    homepage =  https://github.com/kmike/marisa-trie;
+    license = licenses.mit;
+    maintainers = with maintainers; [ ixxie ];
+  };
+}

pkgs/development/python-modules/mecab-python3/default.nix

@@ -0,0 +1,24 @@
+{ lib
+, buildPythonPackage
+, mecab
+, fetchPypi
+}:
+
+buildPythonPackage rec {
+  pname = "mecab-python3";
+  version = "0.7";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "007dg4f5fby2yl7cc44x6xwvcrf2w2ifmn0rmk56ss33mhs8l6qy";
+  };
+
+  propagatedBuildInputs = [ mecab ];
+
+  meta = with lib; {
+    description = "A python wrapper for mecab: Morphological Analysis engine";
+    homepage =  https://github.com/LuminosoInsight/wordfreq/;
+    license = licenses.bsd0;
+    maintainers = with maintainers; [ ixxie ];
+  };
+}

pkgs/development/python-modules/parse-type/default.nix

@@ -6,21 +6,13 @@
 
 buildPythonPackage rec {
   pname = "parse_type";
-  version = "0.3.4";
+  version = "0.4.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "3dd0b323bafcb8c25e000ce5589042a1c99cba9c3bec77b9f591e46bc9606147";
+    sha256 = "0g3b6gsdwnm8dpkh2vn34q6dzxm9gl908ggyzcv31n9xbp3vv5pm";
   };
 
-  patches = [
-    (fetchpatch {
-      name = "python-3.5-tests-compat.patch";
-      url = "https://github.com/jenisys/parse_type/pull/4.patch";
-      sha256 = "1mmn2fxss6q3qhaydd4s4v8vjgvgkg41v1vcivrzdsvgsc3npg7m";
-    })
-  ];
-
   checkInputs = [ pytest pytestrunner ];
   propagatedBuildInputs = [ parse six ] ++ stdenv.lib.optional (pythonOlder "3.4") enum34;
 

pkgs/development/python-modules/parse/default.nix

@@ -3,22 +3,14 @@
 }:
 buildPythonPackage rec {
   pname = "parse";
-  version = "1.6.6";
+  version = "1.8.2";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "71435aaac494e08cec76de646de2aab8392c114e56fe3f81c565ecc7eb886178";
+    sha256 = "1lj9v1q4imszyhvipb6drsm3xdl35nan011mqxxas1yaypixsj40";
   };
 
-  patches = [
-    (fetchpatch {
-      name = "python-3.5-tests-compat.patch";
-      url = "https://github.com/r1chardj0n3s/parse/pull/34.patch";
-      sha256 = "16iicgkf3lwivmdnp3xkq4n87wjmr3nb77z8mwz67b7by9nnp3jg";
-    })
-  ];
-
   checkPhase = ''
     ${python.interpreter} test_parse.py
   '';

pkgs/development/python-modules/pybindgen/default.nix

@@ -0,0 +1,23 @@
+{ stdenv, fetchPypi, buildPythonPackage, setuptools_scm, pygccxml }:
+buildPythonPackage rec {
+  pname = "PyBindGen";
+  version = "0.18.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1sl4jn8rildv6f62cab66w791cixhaaxl7gwg9labs099rl74yl6";
+  };
+
+  buildInputs = [ setuptools_scm ];
+
+  checkInputs = [ pygccxml ];
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/gjcarneiro/pybindgen;
+    description = "Python Bindings Generator";
+    license = licenses.lgpl2;
+    maintainers = with maintainers; [ teto ];
+  };
+}
+
+

pkgs/development/python-modules/pygccxml/default.nix

@@ -0,0 +1,26 @@
+{ stdenv, castxml, fetchFromGitHub, buildPythonPackage,
+llvmPackages, clang }:
+buildPythonPackage rec {
+  pname = "pygccxml";
+  version = "1.9.1";
+
+  src = fetchFromGitHub {
+    owner  = "gccxml";
+    repo   = "pygccxml";
+    rev    = "v${version}";
+    sha256 = "02ip03s0vmp7czzflbvf7qnybibfrd0rzqbc5zfmq3zmpnck3hvm";
+  };
+
+  buildInputs = [ castxml llvmPackages.libcxxStdenv];
+
+  # running the suite is hard, needs to generate xml_generator.cfg
+  # but the format doesn't accept -isystem directives
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/gccxml/pygccxml;
+    description = "Python package for easy C++ declarations navigation";
+    license = licenses.boost;
+    maintainers = with maintainers; [ teto ];
+  };
+}

pkgs/development/python-modules/rootpy/default.nix

@@ -1,4 +1,4 @@
-{ lib, fetchPypi, isPy3k, buildPythonPackage, numpy, matplotlib, root, root_numpy, tables }:
+{ lib, fetchPypi, isPy3k, buildPythonPackage, numpy, matplotlib, root, root_numpy, tables, pytest }:
 
 buildPythonPackage rec {
   pname = "rootpy";
@@ -14,6 +14,14 @@ buildPythonPackage rec {
 
   propagatedBuildInputs = [ matplotlib numpy root root_numpy tables ];
 
+  checkInputs = [ pytest ];
+  checkPhase = ''
+    # tests fail with /homeless-shelter
+    export HOME=$PWD
+    # skip problematic tests
+    py.test rootpy -k "not test_stl and not test_cpp and not test_xrootd_glob_single and not test_xrootd_glob_multiple"
+  '';
+
   meta = with lib; {
     homepage = http://www.rootpy.org;
     license = licenses.bsd3;

pkgs/development/python-modules/tensorflow/bin.nix

@@ -0,0 +1,51 @@
+{ stdenv
+, lib
+, fetchurl
+, buildPythonPackage
+, isPy3k, isPy36, pythonOlder
+, numpy
+, six
+, protobuf
+, absl-py
+, mock
+, backports_weakref
+, enum34
+, tensorflow-tensorboard
+, cudaSupport ? false
+}:
+
+# tensorflow is built from a downloaded wheel because the source
+# build doesn't yet work on Darwin.
+
+buildPythonPackage rec {
+  pname = "tensorflow";
+  version = "1.5.0";
+  format = "wheel";
+
+  src = fetchurl {
+    url = "https://storage.googleapis.com/tensorflow/mac/cpu/tensorflow-${version}-py3-none-any.whl";
+    sha256 = "1mapv45n9wmgcq3i3im0pv0gmhwkxw5z69nsnxb1gfxbj1mz5h9m";
+  };
+
+  propagatedBuildInputs = [ numpy six protobuf absl-py ]
+                 ++ lib.optional (!isPy3k) mock
+                 ++ lib.optionals (pythonOlder "3.4") [ backports_weakref enum34 ]
+                 ++ lib.optional (pythonOlder "3.6") tensorflow-tensorboard;
+
+  # tensorflow depends on tensorflow_tensorboard, which cannot be
+  # built at the moment (some of its dependencies do not build
+  # [htlm5lib9999999 (seven nines) -> tensorboard], and it depends on an old version of
+  # bleach) Hence we disable dependency checking for now.
+  installFlags = lib.optional isPy36 "--no-dependencies";
+
+  meta = with stdenv.lib; {
+    description = "Computation using data flow graphs for scalable machine learning";
+    homepage = http://tensorflow.org;
+    license = licenses.asl20;
+    maintainers = with maintainers; [ jyp abbradar ];
+    platforms = platforms.darwin;
+    # Python 2.7 build uses different string encoding.
+    # See https://github.com/NixOS/nixpkgs/pull/37044#issuecomment-373452253
+    broken = cudaSupport || !isPy3k;
+  };
+}

pkgs/development/python-modules/tensorflow/default.nix

@@ -149,7 +149,7 @@ in buildPythonPackage rec {
     homepage = http://tensorflow.org;
     license = licenses.asl20;
     maintainers = with maintainers; [ jyp abbradar ];
-    platforms = with platforms; if cudaSupport then linux else linux ++ darwin;
+    platforms = platforms.linux;
     broken = !(xlaSupport -> cudaSupport);
   };
 }

pkgs/development/python-modules/wordfreq/default.nix

@@ -0,0 +1,48 @@
+{ lib
+, buildPythonPackage
+, regex
+, langcodes
+, ftfy
+, msgpack
+, mecab-python3
+, jieba
+, nose
+, pythonOlder
+, fetchFromGitHub
+}:
+
+buildPythonPackage rec {
+  pname = "wordfreq";
+  version = "2.0";
+
+   src = fetchFromGitHub {
+    owner = "LuminosoInsight";
+    repo = "wordfreq";
+    rev = "e3a1b470d9f8e0d82e9f179ffc41abba434b823b";
+    sha256 = "1wjkhhj7nxfnrghwvmvwc672s30lp4b7yr98gxdxgqcq6wdshxwv";
+   };
+
+  checkInputs = [ nose ];
+
+  checkPhase = ''
+    # These languages require additional dictionaries
+    nosetests -e test_japanese -e test_korean -e test_languages
+  '';
+   
+  propagatedBuildInputs = [ regex langcodes ftfy msgpack mecab-python3 jieba ];
+  
+  # patch to relax version requirements for regex
+  # dependency to prevent break in upgrade
+  postPatch = ''
+    substituteInPlace setup.py --replace "regex ==" "regex >="
+  '';
+    
+  disabled = pythonOlder "3";
+
+  meta = with lib; {
+    description = "A library for looking up the frequencies of words in many languages, based on many sources of data";
+    homepage =  https://github.com/LuminosoInsight/wordfreq/;
+    license = licenses.mit;
+    maintainers = with maintainers; [ ixxie ];
+  };
+}